1. Chapter 19 Regulation of Gene Expression in Eukaryotes
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2. Chapter Outline
Ways of Regulating Eukaryotic Gene Expression: An Overview
Induction of Transcriptional Activity by Environmental and Biological Factors
Molecular Control of Transcription in Eukaryotes
Posttranscriptional Regulation of Gene Expression by RNA Interference
Gene Expression and Chromatin Organization
Activation and Inactivation of Whole Chromosomes
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3. Ways of Regulating Eukaryotic Gene Expression: An Overview
Eukaryotic gene expression can be regulated at the transcriptional, processing, or translational levels.
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4. Eukaryotic Gene Expression
-Capping 5’ polyAed at 3”
-RNA Splicing
-Compartmentalization
-Regulation ?
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5. Controlled Transcription of DNA
Eukaryote:
Both intracellular signaling and intercellular communication are important for transcriptional regulation in eukaryotes (cell surface to nucleus).
Positive and negative regulator proteins called transcription factors bind to specific regions of DNA and stimulate or inhibit transcription.
Prokaryote:
Protein/DNA interaction: negative (lac repressor) and positive ( CAP/cAMP)
RNA polymerase
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6. Alternate Splicing of RNA
Splicing:-removing introns-spliceosomes
Alternate splicing of transcripts makes it possible for a single gene to encode several polypeptides.
is a prominent mechanism to generate protein diversity.
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7. Alternate Splicing of the Rat Troponin T Gene
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8. Cytoplasmic Control of mRNA Stability
mRNA degradation
mRNA stability is influenced by several factors
The poly(A) tail
The sequence of the 3’UTR
Chemical factors (e.g., hormones)
Small interfering RNAs (siRNAs) or microRNAs (miRNAs)
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9. Induction of Transcriptional Activity by Environmental and Biological Factors
Eukaryotic gene expression can be induced by environmental factors such as heat and by signaling molecules such as hormones and growth factors.
Lactose- inducer
Tryptophan- repressor
bacteria
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10. The Heat-Shock Genes (Proteins)
When organisms are subjected to the stress of high temperature, they synthesize a group of proteins (the heat-shock proteins) that help to stabilize the internal cellular environment.
The expression of the heat-shock proteins is regulated at the transcriptional level; transcription of the heat-shock genes is induced by heat.
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11. Induction of the Drosophila hsp70 Gene by Heat Shock
36.7 to 37ºC
41 to 42ºC
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12. Regulation of Gene Expression by Steroid Hormones
Transcription factors
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13. Regulation of Gene Expression by Peptide Hormones
Signal transduction
(several)
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14. Hormone Response Elements
Hormone response elements (HREs) are analogous to the heat-shock response elements.
HREs are DNA specific sequences located near the genes they regulate that bind specific proteins that act as transcription factors.
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15. Activation of Transcription by Hormones
A steroid hormone/cytosolic receptor complex binds to the HRE sequence to stimulate transcription.
For peptide hormones, the receptor stays at the cell membrane; the signal is conveyed through the cytoplasm by other proteins, causing a transcription factor to bind to a regulatory sequence near a gene.
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16. Molecular Control of Transcription in Eukaryotes
The transcription of eukaryotic genes is regulated by interactions between proteins and DNA sequences within or near the genes.
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17. DNA Sequences that Control Transcription
Basal transcription factors are proteins that bind to specific DNA sequences within the promoter to facilitate RNA polymerase alignment.
Special transcription factors are proteins that bind to response elements or to sequences called enhancers that are located near a gene and facilitate the action of basal transcription factors and RNA polymerase.
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18. Properties of Enhancers
Enhancers act over relatively large distances.
The influence of an enhancer of gene expression is independent of orientation.
The effects of enhancers are independent of position. They may be upstream, downstream, or within an intron.
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19. Tissue-Specific Enhancers of the Drosophila yellow Gene
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20. There Are Several Types of Transcription Factors
Basal factors (TFs) and RNA polymerase bind to promoter and TATAA box.
Activators are proteins that recognize specific short DNA sequences inducing the efficiency of the promoters.
Co-activators are proteins required for a more efficient transcription. They do not bind DNA.
Regulators of chromatin structure
Figure 25.2

21. Regulation of Transcription by Enhancers
Proteins that bind to enhancers influence the activity of proteins that bind to promoters, including the basal transcription factors and RNA polymerase.
These proteins are brought into contact with one another by the mediator complex.
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22. Proteins That Control Transcription
Transcription factors usually have two domains (fragment) that may be in separate parts of the molecule or overlapping
A DNA binding domain that binds the enhancer
A transcriptional activation domain
A transcription factor bound to an enhancer element may interact with other proteins bound at enhancers or with proteins bound at the promoter to facilitate RNA polymerase alignment.
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23. Structural Motifs (smaller fragment) of Transcription Factors
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24. -----control elements
Anatomy of a Typical Eukaryotic Gene, with Its Core Promoter and Proximal Control Region
-----control elements
Enhancer
Silencer
monocistronic

25. Model for Enhancer Action
Suppressor or silencer
DHAC: De-acetylase complex
MTC: Methyl transferase complex
Co-repressor
HAT: histone acetyl transferase
Co-activator
Remodeling complex

26. Combinatorial Model for Gene Expression

27. Post-transcriptional Regulation of Gene Expression by RNA Interference
Short noncoding RNAs may regulate the expression of eukaryotic genes by interacting with the messenger RNAs produced by these genes.
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28. RNA Interference
Small, noncoding RNAs base pair with target sequences in mRNA.
The small RNAs interfere with expression of the target mRNAs.
RNAi has been documented in C. elegans, Drosophila, Arabidopsis, and in mammals, including humans.
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31. MicroRNAs
Some molecules that induce RNAi are derived from microRNA (mir) genes.
The mir transcript forms a stem-loop structure that is processed by the enzymes Drosha and Dicer to form an miRNA
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32. Sources of siRNA and miRNA
miRNAs are derived from endogenous transcripts of the mir genes.
Long double-stranded RNA that is transfected or injected into a cell can be processed to form an siRNA. This can be used experimentally to knock down expression of a gene.
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33. Gene Expression and Chromatin Organization
Various aspects of chromatin organization influence the transcription of genes.
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34. Chromatin packaging: Eu- or hetero-chromatin
Position-effect variegation:
change in the position of the interaction of DNA/histones may
move the conversion of eu- to hetero-chromatin
Eye color phenotype
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35. Molecular Organization of Transcriptionally Active DNA
Transcriptionally active DNA is more sensitive to DNase I than non-transcribed DNA.
The nuclease sensitivity of transcriptionally active genes depends on the presence of two small nonhistone proteins, HMG14 and HMG17.
The promoter and enhancer regions of active genes contain DNase I hypersensitive sites.
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36. The -Globin Gene Cluster
The locus control region (LCR) contains several DNase I hypersensitive sites.
The -globin genes are spatially and temporally regulated.
The LCR is dependent on orientation, unlike enhancer elements.
The LCR insulates the -globin genes from nearby chromatin.
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37. Chromatin Remodeling
In preparation for transcription, nucleosomes are altered by multiprotein complexes in a process called chromatin remodeling.
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38. Types of Chromatin Remodeling Complexes
Histone acetyl transferases (HATs) transfer acetyl groups to lysine side chains on histone proteins.
Other remodeling complexes disrupt nucleosome structure near a gene’s promoter by sliding or transferring histone octamers to new locations (e.g., the yeast SNI/SNF complex)
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39. Reverse Remodeling
Active chromatin can be made inactive by biochemical modifications to histones.
Histone deacetylases (HDACs) remove acetyl groups from histone proteins.
Histone methyl transferases (HMTs) add methyl groups to histone proteins.
DNA methyl transferases (DNMTs) add methyl groups to nucleotides to inactivate transcription.
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40. Euchromatin and Heterochromatin
Heterochromatin stains deeply.
Euchromatin stains more lightly.
Euchromatin contains the majority of eukaryotic genes.
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41. Chromatin Is Divided into Euchromatin and Heterochromatin
Heterochromatin is more
densely packed than
euchromatin
Heterochromatin :
-permanently condensed
-consists in DNA sequence repeats (not transcribed)
-reduced density of genes (inactivated)
-replicates at late states of the S phase.
-interacts with Histones
Regions of heterochromatin remain densely packed throughout interphase.

42. Types of Heterochromatin
Centric heterochromatin is located around the centromeres.
Intercalary heterochromatin is dispersed throughout eukaryotic chromosomes.
Telomeric heterochromatin is located at the ends of the chromosomes.
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43. DNA Methylation
Most methylated cytosines are found in the dinucleotide sequence CG, denoted mCpG.
The restriction enzyme HpaII recognizes and cleaves the sequence CCGG, but cannot cleave the sequence when the second cytosine is methylated.
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44. CpG Islands
CpG dinucleotides occur less often that expected in mammalian genomes, probably due to mutation into TpG dinucleotides over the course of evolution.
The distribution of CpG dinucleotides is uneven.
Most CpG islands are located near transcription start sites; cytosines in these regions are rarely methylated.
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45. Gene Expression Is Associated with DNA De-methylation
Gene expression is associated with de-methylation Me Me

46. Methylated DNA is Associated with Transcriptional Repression
The inactive X chromosome in female mammals is extensively methylated.
Regions of mammalian genomes containing repetitive sequences are methylated.
Proteins that repress transcription have been shown to bind to methylated DNA.
DNA methylation in mammals is responsible for imprinting, in which the expression of a gene is controlled by its parental origin.
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